## [1] "O77_p4_IFNg_R1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
61,280,185 |
61,280,185 |
| Not Truncated |
34,964,752 |
35,780,238 |
| Truncated |
26,315,433 |
25,499,947 |
Truncated Read Length
| Average Length Truncated |
44.5 |
43.7 |
Mapping Efficiency
| Too Short To Map |
5,433,918 |
5,719,737 |
| Unique Alignments |
50,413,656 |
48,288,169 |
| Multiple Alignments |
1,985,585 |
1,786,075 |
| Failed To Align |
3,447,026 |
5,486,204 |
| Paired |
40,683,842 |
40,683,842 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
14,951,895 |
| Invalid Pairs |
25,731,947 |
| Same Circularised |
45,474 |
| Same Dangling Ends |
2,663,670 |
| Same Fragment Internal |
10,168,912 |
| Re Ligation |
10,950,829 |
| Contiguous Sequence |
715,129 |
| Wrong Size |
1,187,933 |
| Total Pairs |
40,683,842 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
14,951,895 |
29,624 |
| Cis-close (<10Kbp) |
1,538,070 |
2,815 |
| Cis-far (>10Kbp) |
8,658,523 |
15,825 |
| Trans |
4,755,302 |
10,984 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data
